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1

Model to Estimate Carbon in Organic

Soils - Sequestration and Emissions

(ECOSSE).

User-Manual

August 2010 Issue

Smith J, Gottschalk P, Bellarby J, Richards M, Nayak D, Coleman K, Hillier J, Flynn H, Wattenbach M,

Aitkenhead M, Yeluripurti J, Farmer J, Smith P

Contact: Jo Smith

Address: Institute of Biological and Environmental Sciences,

School of Biological Sciences,

University of Aberdeen,

23 St Machar Drive, Room G45

Aberdeen,

AB24 3UU,

Scotland,

UK

Tel: +44 (0)1224 272702

Fax: +44 (0)1224 272703

E-mail: jo.smith@abdn.ac.uk

2 WWW: http://www.abdn.ac.uk/ibes/staff/jo.smith/ECOSSE

Contents

PART A - MODEL DESCRIPTION ............................................................................................................. 11

A1 Introduction ..................................................................................................................................... 11

A1.1 Importance of long term estimates of aerobic decomposition ................................................ 11

A1.2 The ECOSSE approach ............................................................................................................... 11

A2 The activity of soil organic matter decomposition .......................................................................... 13

A2.1 Definition of pools used in ECOSSE ........................................................................................... 13

A2.2 Determining the initial sizes of soil organic matter pools ........................................................ 14

A2.2.1 Rapid determination of initial soil organic matter pool sizes ............................................ 14

A2.2.2 Initialization by full ECOSSE simulation .............................................................................. 16

A2.3 Evaluation of the methods used to determine the initial sizes of the soil organic matter pools

........................................................................................................................................................... 17

A3 Aerobic decomposition of soil organic matter pools ....................................................................... 18

A3.1 Impact of soil water on aerobic decomposition ....................................................................... 19

A3.2 Impact of soil temperature on aerobic decomposition ............................................................ 21

A3.3 Impact of soil pH on aerobic decomposition ............................................................................ 21

A3.4 Impact of crop cover on aerobic decomposition ...................................................................... 23

A3.5 Impact of nitrogen on aerobic decomposition ......................................................................... 24

A3.6 Impact of clay content on aerobic decomposition ................................................................... 25

A3.7 Evaluation of ECOSSE simulations of aerobic decomposition .................................................. 26

A4 Anaerobic decomposition of soil organic matter pools ................................................................... 26

A4.1 Impact of soil water on anaerobic decomposition ................................................................... 27

A4.2 Impact of soil temperature on anaerobic decomposition ........................................................ 28

A4.3 Impact of soil pH on anaerobic decomposition ........................................................................ 30

A4.4 Impact of crop cover on anaerobic decomposition .................................................................. 31

A4.5 Impact of nitrogen on anaerobic decomposition ..................................................................... 31

A4.6 Impact of clay content on anaerobic decomposition ............................................................... 31

A4.7 Impact of oxygen on methane emissions ................................................................................. 31

A4.8 Evaluation of ECOSSE simulations of anaerobic decomposition .............................................. 32

A5 Nitrogen transformations ................................................................................................................ 32

A5.1 Mineralisation / Immobilisation ................................................................................................ 32

3

A5.2 Nitrification ............................................................................................................................... 32

A5.3 Denitrification ........................................................................................................................... 35

A5.4 Nitrate leaching ......................................................................................................................... 38

A5.5 Leaching of dissolved organic matter ....................................................................................... 38

A5.6 Ammonia volatilisation ............................................................................................................. 41

A5.6.1 Volatilisation loss from applied manure ............................................................................ 41

A5.6.2 Volatilisation loss from fertiliser ........................................................................................ 42

A5.7 Crop nitrogen uptake ................................................................................................................ 43

A5.7.1 Plant Inputs ........................................................................................................................ 43

A5.7.2 Timing of Management Events .......................................................................................... 43

A.5.7.3 Fertiliser Applications ........................................................................................................ 43

A.5.7.4 Pattern of Debris Incorporation ........................................................................................ 44

A.5.7.5 Pattern of Nitrogen Uptake .............................................................................................. 46

A5.8 Senescence ................................................................................................................................ 46

A5.9 Evaluation of ECOSSE simulations of nitrogen transformations ............................................... 46

A6 Water Movement ............................................................................................................................. 47

A6.1 Vertical water movement ......................................................................................................... 47

A6.2 Restricted flow .......................................................................................................................... 47

A6.3 Evaluation of ECOSSE simulations of water movement ........................................................... 48

PART B - SITE SPECIFIC SIMULATIONS ................................................................................................... 48

B1 Input files .......................................................................................................................................... 48

B1.1 Management Data .................................................................................................................... 48

B1.1.1 Input through file MANAGEMENT.DAT .............................................................................. 48

B1.1.2 Input by setup file .............................................................................................................. 49

B1.2. Weather Data ........................................................................................................................... 50

B1.3 Crop Parameters ....................................................................................................................... 50

B1.4 Soil Parameters ......................................................................................................................... 52

B2 Output files ....................................................................................................................................... 52

PART C - LIMITED DATA SITE SIMULATIONS .......................................................................................... 54

C1 Input files .......................................................................................................................................... 54

C1.1 Site and management data ....................................................................................................... 54

C1.2 Weather data ............................................................................................................................ 58

C2 Output files ....................................................................................................................................... 58

PART D - SPATIAL SIMULATIONS ........................................................................................................... 59

4

D1 Input files ......................................................................................................................................... 59

D1.1 File GNAMES.DAT ...................................................................................................................... 59

D1.2 Input File for NPP and Soil Information .................................................................................... 59

D1.3 Format of Input File for LU Information ................................................................................... 60

D1.4 Format of Input File for Soil Codes ........................................................................................... 61

D1.4.1 Non SSKIB Data .................................................................................................................. 61

D1.4.2 SSKIB Data .......................................................................................................................... 62

D1.5 Format of Input File for Future Climate .................................................................................... 63

D1.5.1 Scottish non-SSKIB and SSKIB ............................................................................................ 63

D1.5.2 Format of Input File for Future Rainfall (JULES run) .......................................................... 64

D1.5.3 Format of Input File for Future Temperature (JULES run) ................................................. 64

D1.5.4 Format of Input File for Net Primary Production (JULES run) ............................................ 64

D2 Output files ...................................................................................................................................... 64

D2.1 Format of Output File for Results on 1km2 grid ........................................................................ 64

D2.2 Format of Output File for Results on 20km2 grid ...................................................................... 67

D2.3 Format of Output File for C Change data (͞CHANGE.OUT") ..................................................... 68

D2.4 Format of Climate Change Results file ...................................................................................... 69

D2.5 Format of File for Calculation of Effects of Different Mitigation Options (files named

MIT_A2P.OUT etc) ............................................................................................................................. 69

PART E - REFERENCES ............................................................................................................................ 70

5

Table 1. Symbols used in equations

Symbol Definition Units

decomposition decomposition return to C to soil by plant kg C ha-1 return to C to soil by plant return to C to soil by plant return to C to soil by plant return to C to soil by plant = 1 layer-1 layer-1 layer-1 layer-1 layer-1 Cin Annual organic input to the soil kg C ha-1 yr-1 layer-1 Cin,def Default annual organic input to the soil kg C ha-1 yr-1 layer-1 6

Symbol Definition Units

matter matter the time step kg C ha-1 layer-1 time step t kg C ha-1 layer-1 Ctot,meas Measured total soil carbon kg C ha-1 layer-1 Ctot,sim Simulated total soil carbon kg C ha-1 layer-1

CH4 diffusion and oxidation

݀ Depth of CH4 production cm

݀ୱ୧୬୩ Depth at which soil becomes a net methane sink cm to when water flow is restricted mm layer-1

DOC to BIO

݇୆୍୓ Rate constant for aerobic decomposition of BIO pool time step-1 ݇ᇱ୆୍୓ Rate constant for anaerobic decomposition of BIO pool time step-1 ݇ୈ୓େ Rate constant for decomposition of DOC into BIO time step-1 ݇େǡ୧୬ Rate constant for the incorporation of C in debris before harvest ݇ୈ୔୑ Rate constant for aerobic decomposition of DPM pool time step-1 ݇ᇱୈ୔୑ Rate constant for anaerobic decomposition of DPM pool time step-1 7

Symbol Definition Units

݇ୌ୙୑ Rate constant for aerobic decomposition of HUM pool time step-1 ݇୒ǡ୧୬ Rate constant for the incorporation of N in debris before harvest ݇ᇱୌ୙୑ Rate constant for anaerobic decomposition of HUM pool time step-1 ݇ୖ Rate constant for aerobic decomposition of SOM pool time step-1 ݇ᇱୖ Rate constant for anaerobic decomposition of SOM pool time step-1 ݇ᇱᇱᇱᇱୖ Rate constant for DOC production from SOM pool time step-1 ݇ୖ୔୑ Rate constant for aerobic decomposition of RPM pool time step-1 ݇ᇱୖ୔୑ Rate constant for anaerobic decomposition of RPM pool time step-1 ݉ᇱᇱᇱୠ Denitrification rate modifier due to biological activity ݉ୡ Aerobic decomposition rate modifier due to crop cover ݉ᇱୡ Anaerobic decomposition rate modifier due to crop cover ݉ᇱᇱᇱᇱ௖ Rate modifier due to crop cover for production of DOC ݉ᇱᇱ୒ୌర Nitrification rate modifier due to ammonium ݉ᇱᇱᇱ୒୓ଷ Denitrification rate modifier due to nitrate ݉୮ୌ Aerobic decomposition rate modifier due to soil pH ݉ᇱ୮ୌ Anaerobic decomposition rate modifier due to soil pH ݉ᇱᇱ୮ୌ Nitrification rate modifier due to soil pH ݉ᇱᇱᇱᇱ௣ு Rate modifier due to soil pH for production of DOC ݉୮ୌǡ୫୧୬ Minimum value for aerobic decomposition rate modifier according to pH ݉୲ Aerobic decomposition rate modifier due to soil temperature ݉ᇱ୲ Anaerobic decomposition rate modifier due to soil temperature ݉ᇱᇱ௧ Nitrification rate modifier due to soil temperature ݉ᇱᇱᇱᇱ௧ Rate modifier due to soil temperature for production of DOC ݉୵ Aerobic decomposition rate modifier due to soil moisture ݉ᇱ୵ Anaerobic decomposition rate modifier due to soil moisture ݉ᇱᇱ୵ Nitrification rate modifier due to soil moisture ݉ᇱᇱԢ୵ Denitrification rate modifier due to soil moisture ݉ᇱᇱᇱԢ୵ Rate modifier due to soil moisture for production of DOC ݉୵଴ Aerobic decomposition rate modifier due to soil moisture at permanent wilting point ݉ᇱᇱ୵଴ Nitrification rate modifier due to soil moisture at 8

Symbol Definition Units

permanent wilting point methane cm-1 ݊ The number of the deepest layer in the soil profile denitrification kg N ha-1 layer-1 timestep-1 timestep-1 timestep-1 field capacity ݊୥ୟୱ Proportion of full nitrification lost as gas timestep-1 timestep-1 timestep-1 ݊୒୓ Proportion of full nitrification gaseous loss lost as NO plant kg N ha-1 year-1 plant kg N ha-1 year-1 ݌ୠୟୡ Proportion of bacteria in the soil ݌ୠୟୡǡ୫୧୬ Minimum proportion of bacteria found in the soil ݌୆୍୓ Proportion of BIO produced on aerobic decomposition kg C (kg C decomp.)-1 9

Symbol Definition Units

݌ୡ୪ୟ୷ Proportion of clay in the soil kg clay (kg soil)-1 starts to decrease decomposition starts to decrease rate ୫୧୬ pH at which rate of DOC production is at minimum rate ݌ୌ୙୑ Proportion of HUM produced on aerobic decomposition kg C (kg C decomp.)-1 ݌୧୬ǡ୅ୋ Proportion of N in above ground crop that is incorporated in the soil ݌୧୬ǡ୙ୋ Proportion of N in below ground crop that is incorporated in the soil ݌୒మǡ଴ Proportion of nitrate N to total denitrification at which N2 emissions fall to zero ݌୒୓య Proportions of denitrified gas emitted as N2 according to the nitrate content of the soil ݌୰ Proportion restriction in drainage at a particular site ݌௪ Proportion of denitrified gas emitted as N2 according to the water content of the soil permanent wilting point mm layer-1 the soil at -100 kPa mm layer-1 the permanent wilting point mm layer-1 permanent wilting point mm layer-1 temperature 10

Symbol Definition Units

ݐ Size of the time step seconds

ݑଵ Empirical parameter describing the sigmoid uptake of N by the crop the crop parts of the plant parts of the plant parts of the plant parts of the plant parts of the plant parts of the plant

ݓ Weeks till harvest

7୷୧ୣ୪ୢ Crop Yield t ha-1

11

PART A - MODEL DESCRIPTION

A1 Introduction

A1.1 Importance of long term estimates of aerobic decomposition Climate change, caused by greenhouse gas (GHG) emissions, is one of the most serious threats facing

our planet, and is of concern at both UK and devolved administration levels. Accurate predictions for

the effects of changes in climate and land use on GHG emissions are vital for informing land use policy. Models that are currently used to predict differences in soil carbon (C) and nitrogen (N) has been suggested that none of these models is entirely satisfactory for describing what happens to organic soils following land-use change. Globally peatland covers approximately 4 million km², with a total C stock of ~450 Pg C in 2008

(Joosten, 2009). Peat is found across the planet with Russia, Canada, Indonesia and the United States

having the largest peatland areas totalling just under 3 million km² (Joosten, 2009). Northern

peatlands are the most important terrestrial C store. It is estimated that 20-30% of the global

terrestrial C is held in 3% of its land area (Gorham, 1991). Over the Holocene, northern peatlands

have accumulated C at a rate of 960 Mt C yr-1 on average, making this ecosystem not only a

substantial store of C, but also a large potential sink for atmospheric C (Gorham, 1991). Reports of Scottish GHG emissions have revealed that approximately 15й of Scotland's total emissions come

reduce the major uncertainty in assessing the C store and flux from land use change on organic soils,

especially those which are too shallow to be true peats but still contain a potentially large reserve of

C. In order to predict the response of organic as well as mineral soils to external change we need models that more accurately reflect the conditions of these soils. Here we present a model for both

organic and mineral soils that will help to provide more accurate values of net change to soil C and N

in response to changes in land use and climate and may be used to inform reporting to GHG

inventories. The main aim of the model described here is to simulate the impacts of land-use and climate change on GHG emissions from these types of soils, as well as mineral and peat soils. The

model is a) driven by commonly available meteorological data and soil descriptions, b) able to predict

the impacts of land-use change and climate change on C and N stores in organic and mineral soils,

and c) able to function at national scale as well as field scale, so allowing results to be used to directly

inform policy decisions.

A1.2 The ECOSSE approach

The ECOSSE model was developed to simulate highly organic soils from concepts originally derived for mineral soils in the RothC (Jenkinson and Rayner, 1977; Jenkinson et al. 1987; Coleman and Jenkinson, 1996) and SUNDIAL (Bradbury et al. 1993; Smith et al. 1996) models. Following these established models, ECOSSE uses a pool type approach, describing soil organic matter (SOM) as pools of inert organic matter, humus, biomass, resistant plant material and decomposable plant material

Fig 1a).

12 Fig 1b. Structure of the nitrogen components of ECOSSE Figure 1a. Structure of the carbon components of ECOSSE 13

All of the major processes of C and N turnover in the soil are included in the model, but each of the

processes is simulated using only simple equations driven by readily available input variables,

allowing it to be developed from a field based model to a national scale tool, without high loss of accuracy. ECOSSE differs from RothC and SUNDIAL in the addition of descriptions of a number of processes and impacts that are not important in the mineral arable soils that these models were originally developed for. More importantly, ECOSSE differs from RothC and SUNDIAL in the way that it makes full use of the limited information that is available to run models at national scale. In particular, measurements of soil C are used to interpolate the activity of the SOM and the plant inputs needed to achieve those measurements. Any data available describing soil water, plant inputs, nutrient applications and timing of management operations are used to drive the model and so

better apportion the factors determining the interpolated activity of the SOM. However, if any of this

information is missing, the model can still provide accurate simulations of SOM turnover, although

the impact of changes in conditions will be estimated with less accuracy due to the reduced detail of

the inputs. This novel approach will be discussed further below. In summary, during the decomposition process, material is exchanged between the SOM pools

according to first order rate equations, characterised by a specific rate constant for each pool, and

modified according to rate modifiers dependent on the temperature, moisture, crop cover and pH of the soil. Under aerobic conditions, the decomposition process results in gaseous losses of carbon dioxide (CO2); under anaerobic conditions losses as methane (CH4) dominate. The N content of the

soil follows the decomposition of the SOM (Fig 1b), with a stable C:N ratio defined for each pool at a

given pH, and N being either mineralised or immobilised to maintain that ratio. Nitrogen released from decomposing SOM as ammonium (NH4+) or added to the soil may be nitrified to nitrate (NO3-).

Carbon and N may be lost from the soil by the processes of leaching (NO3-, dissolved organic C (DOC),

and dissolved organic N (DON)), denitrification, volatilisation or crop offtake, or C and N may be

returned to the soil by plant inputs, inorganic fertilizers, atmospheric deposition or organic

amendments. The soil is divided into 5cm layers, so as to facilitate the accurate simulation of these

processes down the soil profile. The formulation and simulation approach used for each of these processes are described in detail below. A2 The activity of soil organic matter decomposition

A2.1 Definition of pools used in ECOSSE

As already discussed, following the approach used in the RothC model (Coleman and Jenkinson,

1996), ECOSSE uses a pool type approach, describing SOM as pools of inert organic matter (IOM),

humus (HUM), biomass (BIO), resistant plant material (RPM) and decomposable plant material (DPM)quotesdbs_dbs45.pdfusesText_45

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